Mostly works. If you've enabled show hidden files, you'll
still get .DS_Store and occasionally another system file there. Also
for some reason PDFs and a few other browser downloads (Firefox) though
I've told it to use ~/MozDownloads.

Virtual desktops: Virtue

I've got Virtue running. I'm finding I use it less and less with
time. Not because I no longer need virtual desktops, but because it's a
really, really bad virtual desktop. Other than transition effects.

The OS X desktop really isn't designed for multiple workstations (or
monitors). That "Infinite height" menu starts to get inconvenient when
it's two monitors over from where I'm at. And neither application
dragging nor app/windows circulation apply particularly well to Virtue.
Plus its own hotkey combo (alt-tab) steals what's a highly ingrained
shortcut to me.

Focus follows mouse

For those of us who want it, it sucks not to have it.

I suspect it would suck just as much if it was on and you couldn't turn
it off. The point here isn't the setting, it's choice.

Throw in a number of other window management gripes...

Max vertical. For a text term, the one thing I want to be able to do,
really, really quickly, and really, really easily, is maxjust the vertical aspect of my
terminal window. On Linux, I'll bind alt-space to this. No-can-do
under OS X.

Resize widget. There's just the nub on the lower right of a window.
Look, we're grownups. Just let me grab any border and resize, OK?

Edges-off-screen-now-what fallback. Under most Linux WMs, alt+left
mouse allows you to grab and move a window that's got sized or
positioned largely off-screen so you can reach its controls. Not
possible on OS X, though selecting "Window -> Maximize" seems to be a
general rescue move. Shouldn't happen, but does.

Raise/lower windows. OS X, like Windows, operates on a raise-only
model. I can't tell a window to drop to the bottom of the
window stack (alt-downarrow generally on my Linux desktop). Plays along
with focus-follows-mouse. While Expose is almost neat enough
on its own, the lack of a lower-window capability really sucks.

Inconsistent maximization. In some apps, the maximize button goes full
screen, in others it just says "get pleasently plump". If I want a
window larger but not full size, I'll just drag it. If I want it to
fill the damned window, Just Do It[tm]. And be consistent.

I could continue. The point isn't any specific list, it's that there
are capabilities not presented in Aqua, for which any number of users
have working habits honed over years, for which OS X denies any
choice.

The irony: my preferred desktop environment is a (slightly tweaked)
WindowMaker configuration. That's right, the NeXT desktop. Not
unghodly sexy to look at, but a breeze to use.

Package manager:I use DarwinPorts. Works great for
me. YMMV.

I think you're missing the point of single-point-of-control management
of all system packages, including config files, dependencies,
and the rest of it. Sure, I've got fink and Darwin Ports. And within
their own limited universes, they rule (but provide just over a quarter
the 20,000 package choices of my Debian system). OS X very clearly
lacks that. I've bumped into limits of packages not ported to OS X, or
not running smoothly (the X11 Mozilla port, urlview, and mutt, to name
three). If I want Debian ... well, I know where to find it.
Duplicating that effort on a proprietary base seems ... silly.

And yes, while it's possible to add proprietary apps under Liinux,
experience suggests that it's not frequently done and there are some
pretty compelling reasons to avoid doing so, ranging from quality of
Free Software alternatives to maintenance and security headaches.
Software under management is pretty painlessly managed.

There's some fairly compelling reasons to suggest that such package
management addressing proprietary packages on a proprietary OS is highly
unlikely (http://linuxmafia.com/~karsten/Rants/spyware.html) .

First-class package manager: Though I use
DarwinPorts for UNIX-based apps, I don't get how having a package
manager put things in its own hardcoded locations (which vary from
distro to distro) is supposed to be more flexible and user-adapting than
letting me drag the app icon wherever I want.

Those who fail to
understand Debian policy are doomed to repeat it...poorly (http://www.debian.org/doc/debian-policy/) . See also
Manoj's
musings (http://people.debian.org/~srivasta/talks/why_debian/talk.html) .

Note that package management doesn't constrain you, the administrator.
You're more than welcome to muck up your system any way you want to,
and in general, suffer the consequences. Rather, package management is
a constraint on what a package maintainer can to your system.

Downloading files to the Desktop:The location for
downloadable files can be set in the web browser

Application logs:Most apps log errors/status to the
console.log file. You can view this from the command line if you like,
but /Applications/Console will show the log files on the system and has
a rather handy filter box.

Lack of freedom: I don't see how you having to
adapt to the system follows from being able to see the source code for
Mail.app.

Strawman. Among the first things I noted on OS X was the lack of /proc.
Not crucially useful, but very, very useful when needed. Even for the
nontechnical user, it's pretty straightforward to create a script to
reap /proc for useful debugging information for use in technical
support. A script I'd written first for my own use and later shared
on a number of user groups was integrated in a prior employers'
professional services support process.

Later, buying OS X for Unix Geeks, there were the sections marked
simply "undocumented". While there may be lacking
documentation for bits of Linux, there are very few areas which areintentionally left obscured.

I find Linux to require far more adapting than OS X (the old
"...it's just picky about it's friends" line). Guess it just depends on
what you're used to.

As has been noted: Linux gives you the choice. I find my own tweakage
for new systems tends to get accomplished pretty quickly (having the
config files to port around helps a lot). I'm still trying to get my
MacBook Pro to work as I'd like it too.

Case-insensitive filesystem:Because having two
files named Readme and README is just plain stupid.

Like it or not it's 1). Unix (and Linux) standard, and can result in
incorrect or undesireable behavior. I find it annoying much the way DOS
/ CPM's swap of '\' for '/' is.

Classic UNIX utilities and resource forks:

Resource forks and other metadata strike me as a really poor idea on
multiuser or distributed (remote filesystme) systems. Rather than
dumping user-specific data all over the system, it should be managed in
a per-user, user-controled, database.

OS upgrades:I don't mind paying people for work.
Sometimes the open source apps are good enough, but I've seen many
projects abandoned because people have to make a living somehow, and I
don't have the time to write code for every single project that's useful
to me.

And I don't mind being paid for mine. SW economics are strange, most FS
development is compensated one way or another, and I've seen any number
of proprietary apps (and OSs) die, either for lack of market interest or
anticompetitive behavior. BeOS, Netscape, WordStar, VMS, Wang,
Ashton-Tate, Lotus... Even where still extant, most of these are mere
shadows of their former selves.

Main Points

You like the fuzzy feeling of having access to the source code, even
if you never use it

There's a very strong dynamic to free software, and GPL'd free software
in particular. Yes, other licenses have their place, and I'm quite
familiar with strategic licensing. But a sufficiently established
[L]GPL base is powerful stuff. I think they understand this in
Redmond...

you don't have any need for software that OS X does really well (e.g.
media apps

Multimedia is a special case for free software. Because of legal
encumberances (many would say illegitimate encumberances), patent and
copyright laws restrict what would appear to be reasonable uses of
software. Panic and megolomania in the film and music industries have
been particularly toxic, and I'm hoping we'll be able to look back on
the present in the not too distant future with mild bemusement. That
said, yes, iTunes and its ilk are well-done. But I can skip through the
FBI blipvert using mplayer ;-)